Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
MC JC	NC_000913	3,815,859	Δ82 bp		[rph]–[rph]	[rph], [rph]

Missing coverage evidence...
			seq id	start	end	size	←reads	reads→	gene	description
*	*	÷	NC_000913	3815859	3815940	82	42 [0]	[0] 44	[rph]–[rph]	[rph],[rph]

New junction evidence
		seq id	position	reads (cov)	reads (cov)	score	skew	freq	annotation	gene	product
*	?	NC_000913	= 3815858	0 (0.000)	41 (0.990)	33/264	0.3	100%	pseudogene (24/48 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH
	?	NC_000913	3815941 =	0 (0.000)					pseudogene (609/669 nt)	rph	ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH

CCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCG  >  NC_000913/3815720‑3815995                                                                                                                                           |                                                                                                                                          ccTGCTTGCTACGCGCAAATTCAATAACCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtc                                                                                                                                       <  1:271203‑M1/143‑5 (MQ=255)               gcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaat                                                                                                                         >  1:25696‑M1/1‑125 (MQ=255)               gcAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaat                                                                                                                         >  1:602725‑M1/1‑125 (MQ=255)                      caagtgtctggcgcgGGTATGGGTTCGTGCCTTCGCTCCTCATCTTATTGTACTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAGATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgc                                                                                                                  <  2:324198‑M1/136‑26 (MQ=255)                               ggCGCTGTTCTGTTTTCGCGCCGTCGCCCCCCTTCTCCCCTTTCTACAGACACAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcg                                                                                                         <  2:692631‑M1/143‑35 (MQ=255)                               ggCGCTGATATGGTGTCATGCCTGCCCTCCTCTTGTTTGTTCTAGCCAAACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcg                                                                                                         <  1:795163‑M1/143‑35 (MQ=255)                                              gcgtgccTTCGCTCCTGATCTTCCTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttc                                                                                          <  1:734998‑M1/140‑50 (MQ=255)                                                                 cTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCCTCTGAcggtccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggcctcttcggcag                                                                       >  1:371129‑M1/1‑75 (MQ=255)                                                                  ttACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGACTTCTGCcgtcccctgcacttcaatgatgcgcccggcttcggtcaccactccgttcatgtcggtctctgcggcagg                                                                      >  2:377277‑M1/1‑74 (MQ=255)                                                                      ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAACATCAGTTCGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtct                                                                  <  1:454879‑M1/143‑74 (MQ=255)                                                                      ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcgtgtcggtcgctgcggcagagagc                                                                  >  1:522012‑M1/1‑70 (MQ=255)                                                                      ttttCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccatgcacttcaatgatgcgccagtcgtcggtcatccctacgctcatgtcggtctctacggcagagtcc                                                                  >  1:449494‑M1/1‑70 (MQ=255)                                                                          ccacaGACCAAGAAAAGGCGTCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaa                                                              <  2:469081‑M1/141‑78 (MQ=255)                                                                           tacatacaAATAAAAGGCGTCTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaac                                                             <  1:640371‑M1/143‑79 (MQ=255)                                                                           tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcctcggtcatcactacgttcatgtcggtccctccggcaccgtctccacc                                                             >  2:495833‑M1/1‑65 (MQ=255)                                                                                aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtatt                                                        <  1:93934‑M1/143‑84 (MQ=255)                                                                                aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacctatt                                                        >  1:773103‑M1/1‑60 (MQ=255)                                                                                 cAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattc                                                       <  2:25696‑M1/143‑85 (MQ=255)                                                                                      agcaggcGACTCATCAGGCGCCTTAAAGATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaattatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagat                                                  <  2:253149‑M1/140‑90 (MQ=255)                                                                                            cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaa                                            >  2:67427‑M1/1‑48 (MQ=255)                                                                                            cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttaaatgagtcacccgtcttccgtcatcactacgttcatgtcggtatctgcggcagcctcctcaacggcttcaacaacgcaaa                                            >  2:58385‑M1/1‑48 (MQ=255)                                                                                             gACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagcgtcttccacgagtggcagatcgcgcac                                           >  2:427504‑M1/1‑47 (MQ=255)                                                                                             gACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggcgtcgacctcagagtcttcaacgtattccagatcgcaaac                                           >  1:757780‑M1/1‑47 (MQ=255)                                                                                                  atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgctt                                      <  1:141185‑M1/143‑102 (MQ=255)                                                                                                  atcaGTCGCCTGAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcaggtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgctc                                      >  2:360472‑M1/1‑42 (MQ=255)                                                                                                   tcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttc                                     >  1:494260‑M1/1‑41 (MQ=255)                                                                                                   tcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtacctcagtaatggtcttcaacgtattccgggtcgcaagccgcttc                                     >  1:544249‑M1/1‑41 (MQ=255)                                                                                                   gcagTCGCCTTAAAAATCAGCTTGCCAGCGCCGCGTCCTGCcgtcgcctgcacgtcaatgatgcgcccgtcttcggtcctcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttc                                     <  1:334390‑M1/142‑103 (MQ=255)                                                                                                    caGTCGCATTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcg                                    <  2:609989‑M1/143‑104 (MQ=255)                                                                                                      gTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaactgcttcgcc                                  >  1:651760‑M1/1‑38 (MQ=255)                                                                                                          ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgctgcgcccgtcttcggtcatcacgacgttcatgtcggtctctgcggcagagtcttcaacttattccagatcgcaaaccgcttcgccgttc                              <  2:107215‑M1/143‑110 (MQ=255)                                                                                                            ttAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtccctgcggcatagtcgtcaaccgattccagaccgcaaaccgcttcgccgttcac                            >  2:262592‑M1/1‑32 (MQ=255)                                                                                                             tAAAAATCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcaca                           >  1:637117‑M1/1‑31 (MQ=255)                                                                                                              aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcgcgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcacacaccccttcgacgttcacaa                          >  2:301450‑M1/1‑30 (MQ=255)                                                                                                              aaaaaTCAGTTTGCCAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcgggctctgcggcagagtcttcaacgtattcaagatcgcaaaccgcttcgccgctcacaa                          >  2:298261‑M1/1‑30 (MQ=255)                                                                                                                          ggcagCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaa              <  2:221674‑M1/141‑126 (MQ=255)                                                                                                                          accaGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgtccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaa              <  2:103816‑M1/142‑126 (MQ=255)                                                                                                                            cAGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaact            >  1:526437‑M1/1‑16 (MQ=255)                                                                                                                             aGCGCCGCCTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactg           >  1:686821‑M1/1‑15 (MQ=255)                                                                                                                              gcgcCGCCTTCTGCcttctccttcacttcaatgattcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtctgcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgc          <  1:241326‑M1/143‑130 (MQ=255)                                                                                                                                 ccgccTTCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcacaattccgacagaaactgcggc       <  1:550109‑M1/143‑133 (MQ=255)                                                                                                                                      ttCTGCcgtcccctgcacttcaatgatgcgcccgtcttcggtcatcactacgttcatgtcggtctctgcggcagagtcttcaacgtattccagatcgcaaaccgcttcgccgttcccaattccggcagacactgcggctacca  >  1:135667‑M1/1‑6 (MQ=255)                                                                                                                                           |                                                                                                                                          CCTGCTTGCTAAGCGCAAATTCAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCCCCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCG  >  NC_000913/3815720‑3815995

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑